Reading made it two wins from two in the FA Women's Continental Tyres League Cup but were made to work hard by Lewes and needed a late Fara Williams hat-trick to seal the spoils.
The former Lionesses star gave the hosts an early lead but Lewes rallied and Ellie Noble's fine curling effort handed them a half-time lead.
Reading's Super League class told eventually, with Williams nodding a winner in the dying embers.
Having forced early pressure on the Lewes goal, Reading eventually broke the deadlock on the 16th minute following a lapse in defensive concentration from the visitors.
Brooke Chaplen intercepted a short backpass, and after her shot was saved by Baker, Williams followed up to finish from ten yards out.
That goal seemed to force Lewes out of their shell and a minute after Rachel Laws saved well with her feet to stop Zoe Ness getting on the scoresheet, she couldn't do anything to prevent Emily Donovan's long-range strike finding the corner to draw the visitors back level on 27 minutes.
With just over ten minutes until half-time, another magnificent strike put Lewes ahead.
Ellie Noble was given time to curl an effort across goal into the far top corner from all of 30 yards, leading to jubilant celebration amongst the visiting players.
As they did in the first half, Reading began the second period on the front foot and equalised through Williams on 55 minutes.
A set-piece came out to the veteran and she didn't think twice before unleashing a thunderbolt on the half-volley which Baker was unable to prevent, despite getting a hand to it.
Despite the visitors clearing off the line twice, the game ended in heartbreak for Lewes as Williams completed her hat-trick and secured the three points for the Royals, meeting Amalie Eikeland's cross with a header at the back post in stoppage time.
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Reading's hat-trick hero Fara Williams said: "I'm disappointed with our performance. For the first 45 minutes we didn't come out the blocks.
"The second half for us was about working hard and showing the fans that we are a team that want to win and pursue it in the right way."
"They were organised, they frustrated us and they threw themselves in front of shots. But we should be more composed in front of goal.
"It's always nice to score. We won the game so I'm happy that the goals contributed to that."
Lewes midfielder Ellie Noble said: "Coming back off the last game, which was a 3-0 defeat to Leicester, we wanted to see a reaction. We wanted to see heart, desire, fight and we really showed it.
"There's lots to learn, but lots to be proud of as well."
"Everything clicked after we got used to how they play. Mentally we were switched on and thought we could compete with them.
"The mentality was to go out and enjoy it and I think that's what got us the goals and got us so close at the end."
Reading (4-3-3): Rachel Laws; Maz Pacheco, Kiera Skeels, Sophie Howard, Kristine Leine; Rachel Rowe, Angharad James, Fara Williams; Brooke Chaplen, Lisa-Marie Utland, Rakel Honnudottir
Substitutes: Jade Moore for Pacheco 45, Amalie Eikeland for Honnudottir 45, Millie Farrow for Utland 68
Substitutes not used: Grace Moloney, Bethan Roberts
Goals: Williams 16, 55, 90
Lewes (4-4-2): Faye Baker; Sophie O'Rourke, Caitlin Hayes, Amy Taylor, Rhian Cleverley; Ella Powell, Ellie Noble, Filippa Savva, Emily Donovan; Zoe Ness, Jess King
Substitutes: Ava Rowbotham for King 85, Sienna Howell for Taylor 90
Substitutes not used: Emma Jones, Dani Lane, Katie Rood
Goals: Donovan 27, Noble 34
Bookings: Cleverley 63
Referee: Louise Sanders